Federal prosecutors will seek the death penalty for a white man accused of killing nine black parishioners in a racially motivated attack at a church in Charleston, South Carolina, last June, the US Justice Department said on Tuesday.

"The nature of the alleged crime and the resulting harm compelled this decision," Attorney General Loretta Lynch said in a statement.

Dylann Roof, 22, is accused of opening fire on June 17, 2015, during Bible study at Charleston's historic Emanuel African Methodist Episcopal Church in a massacre that shook the country and intensified debate over US race relations.

He faces 33 federal charges, including hate crimes, obstruction of religion and firearms offences.

In a court filing, federal prosecutors cited a number of factors for seeking the death penalty, saying Roof singled out victims who were black and elderly, and showed no remorse. They also cited "substantial planning and premeditation".

A friend of Roof, 21-year-old Joseph Meek, pleaded guilty last month to concealing his knowledge of Roof's intention to carry out the attack, saying then that Roof planned the shooting for six months and wanted to start a race war.

Roof's lawyers have said he would agree to plead guilty, rather than face trial if prosecutors ruled out capital punishment. But defence attorney Michael O'Connell declined comment on Tuesday's decision when reached by phone.

Roof also faces the death penalty if convicted on separate, state murder charges in a trial set to begin in January.

The state prosecutor trying the case said last September that some of the victims' families were opposed to a death sentence due to their religious beliefs, while others felt it was appropriate.

Steve Schmutz, an attorney representing families of three victims, said his clients "support whatever decision the US government is making in this case, and I'm sure they support this decision".

Some relatives of the slain worshippers tearfully offered words of forgiveness during Roof's initial court appearance.. Nearly a year later, views diverged on the federal death penalty decision.

"It's a great message being sent by the government that this won't be tolerated," Kevin Singleton, whose mother was among those killed, told the local Post and Courier newspaper.

The relative of another victim cited the Bible in calling for Roof to spend his life in prison rather than die.

Federal prosecutors rarely seek the death penalty against defendants. Only three federal prisoners have been executed in the past half century and none since 2003, according to the Death Penalty Information Center. The best-known of those was Timothy McVeigh, responsible for the 1995 bombing of the Oklahoma City federal building that killed 168 people.

Roof is due back in federal court in Charleston on June 8, when prosecutors are expected to discuss a trial date.